SMTL ID : 1k3b.1

Crystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): Exclusion Domain Added to an Endopeptidase Framework Creates the Machine for Activation of Granular Serine Proteases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.5 Chain B: R.164 Chain C: F.6, L.8 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Water bridges: A:Y.64, A:N.65, C:L.8 Hydrogen bonds: B:R.164 NAG.6: 4 residues within 4Å: Chain D: N.5 Chain E: R.164 Chain F: F.6, L.8 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F, 1 interactions with chain E Water bridges: D:Y.64, D:N.65, F:L.8 Hydrogen bonds: E:R.164 NAG.11: 4 residues within 4Å: Chain G: N.5 Chain H: R.164 Chain I: F.6, L.8 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain I, 1 interactions with chain H Water bridges: G:Y.64, G:N.65, I:L.8 Hydrogen bonds: H:R.164 NAG.16: 4 residues within 4Å: Chain J: N.5 Chain K: R.164 Chain L: F.6, L.8 4 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J, 1 interactions with chain L Hydrogen bonds: K:R.164 Water bridges: J:Y.64, J:N.65, L:L.8

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: S.22, K.38, Y.75, N.109, W.110, A.111 Chain E: F.108 Chain F: L.69 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.22, A:N.109, F:L.69 Salt bridges: A:K.38 SO4.4: 2 residues within 4Å: Chain B: R.20, N.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.21 Salt bridges: B:R.20 SO4.5: 4 residues within 4Å: Chain B: N.21 Chain C: G.36, T.37, G.38 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.21, C:T.37, C:G.38 SO4.7: 8 residues within 4Å: Chain B: F.108 Chain C: L.69 Chain D: S.22, K.38, Y.75, N.109, W.110, A.111 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.22, D:N.109, C:L.69 Salt bridges: D:K.38 SO4.9: 2 residues within 4Å: Chain E: R.20, N.21 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.21 Salt bridges: E:R.20 SO4.10: 4 residues within 4Å: Chain E: N.21 Chain F: G.36, T.37, G.38 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:T.37, F:G.38, E:N.21 SO4.12: 8 residues within 4Å: Chain G: S.22, K.38, Y.75, N.109, W.110, A.111 Chain K: F.108 Chain L: L.69 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:S.22, G:Y.75, G:N.109, L:L.69 Salt bridges: G:K.38 SO4.14: 2 residues within 4Å: Chain H: R.20, N.21 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.21 Salt bridges: H:R.20 SO4.15: 4 residues within 4Å: Chain H: N.21 Chain I: G.36, T.37, G.38 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:T.37, I:G.38, H:N.21 SO4.17: 8 residues within 4Å: Chain H: F.108 Chain I: L.69 Chain J: S.22, K.38, Y.75, N.109, W.110, A.111 5 PLIP interactions: 1 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:L.69, J:S.22, J:Y.75, J:N.109 Salt bridges: J:K.38 SO4.19: 2 residues within 4Å: Chain K: R.20, N.21 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.21 Salt bridges: K:R.20 SO4.20: 4 residues within 4Å: Chain K: N.21 Chain L: G.36, T.37, G.38 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain L Hydrogen bonds: K:N.21, L:T.37, L:G.38

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain B: F.72, P.73, Y.74, Y.117 Chain C: I.59, V.61 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain E: F.72, P.73, Y.74, Y.117 Chain F: I.59, V.61 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain H: F.72, P.73, Y.74, Y.117 Chain I: I.59, V.61 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain K: F.72, P.73, Y.74, Y.117 Chain L: I.59, V.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Turk, D. et al., Structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases. EMBO J. (2001)

Release Date

2002-04-02

Peptides

dipeptydil-peptidase I exclusion domain: ADGJ
dipeptydil-peptidase I light chain: BEHK
dipeptydil-peptidase I heavy chain: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
C

F
C

I
C

L
C

dipeptydil-peptidase I exclusion domain

dipeptydil-peptidase I light chain

dipeptydil-peptidase I heavy chain

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